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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaacttcttatcttgcatagttttccagtatgctaatgatttttttttttttttgctttagctgctgggtacttcactaaattattcatccattctgttttgctgttaagacgctaaagtgtagatattcctttgaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTACCCCTGTGGCTCTAGAGCTTGGTGGAAAATGCCCTGCAATTGTTGATTC

Basic information

species Oryza sativa
transcript LOC_Os11g08300.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g08300.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G118800_T01 (Zea mays), 3'ss of exon 4
gttaacttcttatcttgcatagttttccagtatgctaatgatttttttttttttttgctttagctgctgggtacttcactaaattattcatccatt---ctgttttgctg-------ttaagacgctaaagtgtagatattcctt-----tgaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTACCCCTGTGGCTCTAGAGCTTGGTGGAAAATGCCCTGCAATTGTTGATTC
||  | ||||||      ||   ||| || |       |||||  |    | ||    ||      | |   |  |    |  |  ||   ||||    | |||  ||         ||  ||  || |  |||| ||  |  |       |||  | ||||||  ||||  || || ||||| |||||||||||||| ||||||||||| || || |||||||| ||||||||||| |||| |||||   |||| || ||
gtcgagttcttagtacctatgaattttca-tggctcggtgattcctaggctgttaaatttgtagaaccgtacatgtagtcatgtatttagcccatcacacagttacgcaaatagaaattgggattctgacatgtatattgttttgacgaacgaacttccagGTAATGGAACCGTAGGACGCATCGTGATGGCAGCAGCCGCAAAGCATCTAACTCCGGTGGCTCTGGAGCTTGGTGGGAAATCCCCTGTTGTTGTGGACTC

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G060800_T02 (Zea mays), 3'ss of exon 3
gttaacttcttatcttgcatagttttccagtatgctaatgatttttttttttttttgctttagctgctgggtacttcactaaattattcatccattctgttttgctgttaagacgctaaagtgtagatattcctttgaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTACCCCTGTGGCTCTAGAGCTTGGTGGAAAATGCCCTGCAATTGTTGATTC
                                 |  ||      || || |  | |  |  |     |  || ||| |      || | | |  |      ||| |  | |||  || |  ||||  | || |  ||||  | ||||||  |||| ||| || || ||||||||||||||||| ||||||||||| ||||| || ||||| ||||||||||| |||| |||||  || || |||||
--------------------------------cgaaaacagaaattcttctaatataatcca-----taagtccttga------tactgagctgt---acgttgttcgtgagattctgacatgtatgtgtttcgatgaatttccagGTAATGGAACTGTAGGACGTATAGTGATGGCAGCAGCCGCAAAGCATCTGACCCCGGTAGCTCTGGAGCTTGGTGGGAAATCCCCTGTTATCGTGGATTC

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 6
gttaacttcttatcttgcatagttttccagtatgctaatgatttttttttttttttgctttagctgctgggtacttcactaaattattcatccattctgttttgctgttaagacgctaaagtgtagatattcctttgaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTACCCCTGTGGCTCTAGAGCTTGGTGGAAAATGCCCTGCAATTGTTGATTC
                           || | ||  ||||||||     |  ||||   | | ||    | | |||   |   ||  | |       |  |||||||| ||       |  ||||  | ||     |||  |  |||||| ||||  ||||| || || ||||||||||| ||||||||||| ||||| ||||| ||| | |||||||| || ||||| || |   | ||||||||
---------------------------caatttg--aatgatttagccatcatttt---taaactttatgattctttgtt--tttcatgactaggcttaatttgctgtcaa-------acatgtaactgtt-----gaatttatagGTAGTGGAAGAGTGGGACGAATTGTGATGGCAGCTGCTGCAAAGCACCTTACACCTGTAGCTTTGGAGCTTGGGGGGAAATGTCCAGTTGTCGTTGATTC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29660180|gb|CB656455.1|CB656455
EST:     AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAG                         GTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
genomic: AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAGgttaacttct ... gaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
EST: gi|58594363|gb|CF992671.1|CF992671
EST:     AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAG                         GTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
genomic: AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAGgttaacttct ... gaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
EST: gi|33794991|gb|CF323375.1|CF323375
EST:     AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAG                         GTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
genomic: AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAGgttaacttct ... gaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
EST: gi|58591471|gb|CF989779.1|CF989779
EST:     AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAG                         GTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
genomic: AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAGgttaacttct ... gaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
EST: gi|29665740|gb|CB662015.1|CB662015
EST:     AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAG                         GTAGCGGAAACGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
genomic: AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAGgttaacttct ... gaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
EST: gi|58691193|gb|CK079880.1|CK079880
EST:     AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAG                         GTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
genomic: AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAGgttaacttct ... gaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
EST: gi|25806016|gb|CA761977.1|CA761977
EST:     AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAG                         GTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
genomic: AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAGgttaacttct ... gaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
EST: gi|29645892|gb|CB650899.1|CB650899
EST:     AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAG                         GTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
genomic: AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAGgttaacttct ... gaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
EST: gi|33675797|gb|CF304036.1|CF304036
EST:     GCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAG                         GTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
genomic: GCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAGgttaacttct ... gaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
EST: gi|88199260|gb|CI199110.1|CI199110
EST:     AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAG                         GTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA
genomic: AGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAGgttaacttct ... gaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 62 (upstream exon), 71 (downstream exon)
Score: 73

CCTGAATACGTTGATAGCTCTTGCATAAAAGTGGTGGAGGGAGGCGTTCCAGAAACAACCGCACTCTTAGAACAAAAGTGGGATAAGATCTTCTACACAGgttaacttct ... gaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTACCCCTGTGGCTCTAGAGCTTGGTGGAAAATGCCCTGCAATTGTTGATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattctgttttgctgttaagacgctaaagtgtagatattcctttgaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTACCCCTGTGGCTCTAGAGCTTGGTGGAAAATGCCCTGCAATTGTTGATTC
                      cgctaaa  putative branch site (score: 73)
                                      ttcctttg  putative PPT
                                tagatatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaacttcttatcttgcatagttttccagtatgctaatgatttttttttttttttgctttagctgctgggtacttcactaaattattcatccattctgttttgctgttaagacgctaaagtgtagatattcctttgaaactgcagGTAGCGGAAATGTGGGCCGCATAGTGATGGCAGCAGCTGCAAAGCATCTTACCCCTGTGGCTCTAGAGCTTGGTGGAAAATGCCCTGCAATTGTTGATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA